Protein turnover within a cell is regulated by protein synthesis and degradation. One pathway of protein degradation is autophagy, which is capable of degrading misfolded proteins and damaged organelles. A dysregulation of autophagy has been implicated in various cancers, and neurodegenerative diseases including Parkinson's and Huntington's disease. Due to the importance of autophagy in normal cellular function and its dysregulation in disease states there has been a significantly increased interest in autophagy related research within the last 15 years. Despite the increased interest in autophagy research, very few structures of autophagy related proteins have been determined. Therefore, many of the molecular mechanisms that regulate autophagy, including the mechanism of activation of the Atg1/ULK1 complex, remain to be elucidated. The Atg1/ULK1 is the most upstream complex that regulates autophagy and upon activation serves to initiate autophagy. Inhibition of Atg1/ULK1 complex activation results in the near complete inhibition of autophagy demonstrating that the Atg1/ULK1 complex is a master regulator of autophagy. Our goal is to understand the molecular mechanisms that regulate the initiation of autophagy by the Atg1/ULK1 complex, which will provide the molecular basis for the induction of autophagy. To this end, I will perform a structural and functional characterization of the inactive and active forms of the Atg1/ULK1 complex. This work will include structure determination of the Atg1/ULK1 complex as well as a structure driven mutational analysis of the complex to validate and further investigate possible mechanisms for complex activation. Additionally, autophagy has been shown to be induced by pharmaceutical drugs that are used to slow tumor progression. As a result, this work will not only reveal the molecular mechanisms for the induction of autophagy but may also drive future drug design towards targeting the Atg1/ULK1 complex to induce autophagy with higher specificity.